The present invention relates to methods of identifying gene sequences of potential vaccine antigens. Also included are gene sequences and the polypeptides encoded by the gene sequences as well as the use of such sequences to induce a protective immune response in animals. Particularly, the invention relates to identifying potential antigen gene sequences of Mycoplasma, preferably Mycoplasma hyopneumoniae. 
The success of a vaccine to a pathogen resides in identifying a suitable antigen of a pathogen which is readily accessible to a host immune system. Once identified, it can form the basis for protection against the pathogen.
In recent years a number of vaccines have been commercialised by Animal Health companies. Many of the vaccines are based on inactivated whole cell bacterins. Although these vaccines provide a reasonable level of efficacy there is considerable scope for improvement. Therefore the presently available vaccines could be improved on by developing vaccines that were not based on whole cells or fractions of whole cells.
Other means of generating vaccines against pathogens includes the use of crude inactivated antigen mixtures of various proteins. However, the problem with these methods is that they present to the host a variety of antigens, none of which may provide suitable overall protection since the proteins most readily accessible to a host immune system are swamped by the other antigens. Moreover, some pathogens are difficult or expensive to grow because of their fastidious requirements. Some pathogens are also harmful to handle. Therefore, a vaccine which does not require the growing of the cells or bacteria and the processing of whole cells or fractions of whole cells would provide a safer, cheaper and possibly more efficacious vaccine.
One way of achieving a cleaner and more specific vaccine is by using recombinant protective antigens. By providing specific antigens, only those antigens readily accessible to the host immune system may be used.
There is the problem of identifying potential antigens. One way is to create a gene library. However, from the library, it is very time consuming to determine those sequences which may include a potential protective antigen.
To efficiently screen through a large number of potential antigen genes for their efficacy in providing some level of protection from disease it is useful to initially clone them as expressing clones. In this way the need for tedious and time consuming clone analysis and subsequent expression subcloning is avoided. The whole process of antigen discovery is speeded up. Applicants now provide a novel method to ensure that the clones initially investigated were expressing recombinant protein.
Previously, expression libraries have been screened for clones expressing all or part of a specific protein by using an antibody specific for or enriched for the protein of interest.
Identifying the DNA sequences that code for the proteins, also makes it possible, using appropriate expression vehicles, to form recombinant DNA molecules and to transform appropriate hosts (eg., prokaryotic or eukaryotic hosts) with those recombinant DNA molecules. Culturing of the transformed hosts then permits the hosts to express the DNA sequences and to produce the desired proteins.
Administering the produced and subsequently isolated proteins, active ingredients or combinations thereof (eg., by injection), in an amount sufficient to elicit a protective immune response, provides a means for immunising against infections.
One pathogen for which vaccines have been commercialised by Animal Health companies is Mycoplasma hyopneumoniae. This pathogen causes Enzootic pneumonia in pigs. It rarely causes death, but often results in severe morbidity and reduced performance manifesting in significant depression in feed conversion efficiency resulting in reduced weight gain in pigs. The animals show symptoms of coughing and fever and are often prone to secondary infection by opportunistic microorganisms.
Numerous attempts to provide a vaccine against Mycoplasina hyopneumoniae have not been terribly successful. Particularly, the use of heat inactivated, live or extract of Mycoplasma have proven to be ineffective in providing protection. Some vaccines based on inactivated whole cell bacterins have shown some level of efficacy but there is scope for improvement.
Additionally, Mycoplasma hyopneumoniae is difficult and expensive to grow because of its fastidious requirements. Therefore the presently available vaccines could be improved on by developing vaccines that were not based on whole cells or fractions of whole cells.
Accordingly, it is an object of the present invention to overcome or at least alleviate some of the problems of the prior art.
In one aspect of the present invention there is provided a method of identifying expression proteins translated from a nucleotide sequence in an expression vector, said method comprising the use of a marker co-expressed with a protein translated from the nucleotide sequence.
In a preferred embodiment of the present invention there is provided a use of a polyHis tag for identifying expression proteins encoded by a nucleotide sequence in an expression vector wherein said polyHis tag is co-expressed with said protein.
In another aspect of the present invention there is provided a method for identifying expression proteins encoded by a nucleotide sequence from a mixture of nucleotide sequences, said method comprising the steps of:
providing an expression vector including a marker;
introducing a nucleotide sequence from the mixture into the expression vector; and
identifying an expression protein expressed by the expression vector by determining the presence of a fusion protein comprising the marker co-expressed with the expression protein.
In a preferred embodiment the marker is a polyHis tag.
In a further preferred embodiment, the expression vector is transfected into a host cell for expression of a marker-fusion protein comprising an expression protein. Preferably the marker fusion protein is a polyHis tag-fusion protein comprising a polyHis tag and an expression protein. Introduction of a population of expression vectors into the host cell may create a genomic or cDNA library which may be screened.
In a further preferred embodiment of the method there is included a step of purifying the expression protein using the marker expressed in the fusion protein. Preferably the marker is a polyHis tag.
There is provided in another aspect, a purified recombinant protein identified according to the above method. Preferably the recombinant protein is an expression protein.
In another aspect, there is provided a purified nucleotide sequence which encodes a recombinant protein identified according to the above method.
In another aspect of the present invention there is provided an expression vector including a marker, preferably a polyHis tag for use in identifying expression proteins encoded by a nucleotide sequence.
In yet another aspect of the invention, there is provided a host including an expression vector, said vector including a marker, preferably a polyHis tag for use in identifying an expression protein.
In a further aspect of the present invention, there is provided a method of identifying gene sequences encoding antigenic proteins from a sample of nucleotide sequences, said method comprising the steps of:
providing an expression vector including a marker;
introducing a nucleotide sequence from the sample into the expression vector;
identifying an antigenic expression protein expressed by the expression vector by determining the presence of a fusion protein comprising a marker co-expressed with the expression protein translated by the nucleotide sequence; and
identifying the antigenic expression protein.
Preferably the marker is a polyHis tag.
In a preferred embodiment, the method further includes determining the gene sequence of the antigenic protein encoded by the expression vector.
In another aspect of the invention there is provided a method of screening a library of nucleotide sequences, said method including the steps of:
providing a source of nucleotide sequences;
providing an expression vector including a marker;
creating a library by introducing a nucleotide sequence into the expression vector;
identifying an expression protein expressed by the expression vector by determining the presence of a fusion protein comprising a marker co-expressed with the expression protein translated by the nucleotide sequence; and
determining the nucleotide sequence of the expression protein.
Preferably the marker is a polyHis tag.
In another aspect, there is provided a method of screening to identify expression clones in an expression library wherein said method includes:
providing a source of nucleotide sequence;
providing an expression vector including a marker;
introducing the nucleotide sequence into the expression vector;
transforming the expression vector into a host to create an expression library; and
locating an expression clone by detecting the expression of a fusion protein, comprising a marker, preferably a polyHis tag co-expressed with an expression protein.
In a further aspect of the present invention there is provided a method of identifying a therapeutic antigenic gene sequence encoding a therapeutic antigenic protein of a disease, from a sample of nucleotide sequences, said method comprising the steps of:
providing an expression vector including a marker;
introducing a nucleotide sequence from the sample into the expression vector;
identifying an antigenic expression protein expressed by the expression vector by determining the presence of a fusion protein comprising a marker, co-expressed with the expression protein translated by the nucleotide sequence;
inoculating an animal with the expression vector which expresses the antigenic expression protein;
challenging the animal with the disease;
identifying an expression vector and expression protein that provides a therapeutic effect induced by vaccination; and
determining the gene sequence of the antigenic expression protein encoded by the expression vector.
Preferably the marker is a polyHis tag.
In a further preferred embodiment of the invention, there is provided a method of screening a library of nucleotide sequences for a nucleotide sequence encoding polypeptides of Mycoplasma, preferably Mycoplasma hyopneumoniae, said method comprising the steps of:
providing a source of nucleotide sequences from a sample of Mycoplasma;
providing an expression vector including a marker;
introducing a nucleotide sequence into the expression vector;
identifying a Mycoplasma expression protein expressed by the expression vector by determining the presence of a fusion protein comprising a marker, preferably a polyHis tag, co-expressed with the expression protein translated by a nucleotide sequence; and
determining the nucleotide sequence of the expression protein of Mycoplasma, preferably Mycoplasma hyopneumoniae. 
Preferably the marker is a polyHis tag.
In a preferred embodiment, the gene sequence encodes an antigenic polypeptide of Mycoplasma, preferably Mycoplasma hyopneumoniae. 
In yet another aspect of the present invention, there is provided a nucleotide sequence, mutant, analogue, derivative or functionally active fragment thereof encoding a polypeptide of Mycoplasma, preferably Mycoplasma hyopneumoniae, said nucleotide sequence identified by the methods described above. Preferably the nucleotide sequence composes a sequence according to any one of FIGS. 1 to 42, and mutants, analogues derivatives or functionally active fragments thereof. More specifically, the nucleotide sequence is according to SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 21, SEQ ID NO: 23, SEQ ID NO: 25, SEQ ID NO: 27, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO;33, SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 43, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO: 59, SEQ ID NO: 61, SEQ ID NO: 63, SEQ ID NO: 65, SEQ ID NO: 67, SEQ ID NO: 69, SEQ ID NO: 71, SEQ ID NO: 73, SEQ ID NO: 75, SEQ ID NO: 77, SEQ ID NO: 79, SEQ ID NO: 81 or SEQ ID NO: 83 or a mutant, analogue, derivatives or functionally active fragments thereof.
In an even further aspect of the present invention, there is provided a polypeptide encoded by the nucleotide sequence mutant, analogue, derivatives or functionally active fragments thereof encoding a polypeptide of Mycoplasma, preferably Mycoplasma hyopneumoniae, said nucleotide sequence identified by the methods described above. Preferably the polypeptide is encoded by a nucleotide sequence encoded by a sequence according to any one of FIGS. 1 to 42, mutant, analogues, derivatives or functionally active fragment thereof. More specifically the polypeptide has an amino acid sequence according to SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 34, SEQ ID NO: 36, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 72, SEQ ID NO: 74, SEQ ID NO: 76, SEQ ID NO: 78, SEQ ID NO: 80, SEQ ID NO: 82 or SEQ ID NO: 84 or a mutant, analogue, derivatives or functionally active fragments thereof.
In a further aspect of the present invention, there is included compositions comprising the polypeptides or nucleotide sequences described above. Furthermore in other aspects, there is included pharmaceutical compositions and vaccine compositions of the polypeptide or nucleotide sequences described above.
Other aspects of the invention include monoclonal antibodies generated against the polypeptides.
Also included as a further aspect of the invention is a method of treating Mycoplasma infection, said method including administering an effective amount of an antigen polypeptide of Mycoplasma encoded by a nucleotide sequence or nucleotide sequence encoding the polypeptide identified by the methods above. Preferably, the antigen polypeptide is encoded by a nucleotide sequence according to any one of FIGS. 1 to 42 or a mutant, analogue, derivative or functionally active fragment thereof. More specifically the nucleotide sequence is according to SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO;15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 21, SEQ ID NO: 23, SEQ ID NO: 25, SEQ ID NO: 27, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 33, SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 43, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO: 59, SEQ ID NO: 61, SEQ ID NO: 63, SEQ ID NO: 65, SEQ ID NO: 67, SEQ ID NO: 69, SEQ ID NO: 71, SEQ ID NO: 73, SEQ ID NO: 75, SEQ ID NO: 77, SEQ ID NO: 79, SEQ ID NO: 81 or SEQ ID NO: 83 or a mutant, analogue, derivatives or functionally active fragments thereof.
Throughout the description and claims of this specification, the word xe2x80x9ccomprisexe2x80x9d and variations of the word, such as xe2x80x9ccomprisingxe2x80x9d and xe2x80x9ccomprisesxe2x80x9d, is not intended to exclude other additives, components, integers or steps.